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Old 07-31-2014, 03:41 AM   #1
hbt
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Question Producing associated gene lists.......?

Does anyone know the best way to produce a list of genes (official gene ID preferably) that have the same associated function.

for example i want to get a comprehensive list of official gene IDs for genes known to be cytokines. (in human)

I assume I would need to find a broad GO-term that would include all cytokines, but I don't know how to produce a list which includes the official gene ID only.

many thanks
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Old 07-31-2014, 04:08 AM   #2
Richard Finney
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Get these files : gene2go and gene_info from NCBI

You can use these commands from command line...
wget -nc ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
wget -nc ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

Uncompress them using "gzip -d filename.gz".

gene2go has the id to goterm
gene_info has the id to gene name.
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Old 07-31-2014, 04:11 AM   #3
k.devito
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NCBI could be helpful. Enter "gene" next to the search bar and search "cytokine", narrow down your query by clicking on "Homo sapiens"/ whatever species you're using in the sidebar after completing your search. From there you can click on the genes of interest and create a txt file with the information you want to download. Is this helpful at all/what you were looking for?

EDIT: Ah, previous poster beat me to the punch .
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Old 07-31-2014, 04:13 AM   #4
GenoMax
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Search for cytokine at: http://www.proteinatlas.org/ You should be able to download a tab delimited list from the results.
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Old 07-31-2014, 04:28 AM   #5
hbt
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That's great, thank you all
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